[Xplor-nih] rna database potential refinement

[John Kuszewski]

Hi Gokul,

Could you send me the relevant output?

Most likely, it just means that the minimizer got stuck.  The  
gradients from the orie and rama terms are approximate, because  
they're coming from databases of known structures, and so they can  
occasionally be too rough for the minimizer.

If all the experimental terms (NOE, RDC, etc) have acceptable  
agreements, then you can probably take the final coordinates from  
your rama + orie structures as converged.

--JK

On Mar 3, 2008, at 12:33 PM, Gokul Ramaswami wrote:

> Hello Xplor users,
>
> I am trying to refine an rna molecule using the rama and orie database
> potentials.  The problem is during the final minimization I get an
> error message stating that the gradient may be incorrect and the
> program terminates.  If I take out these 2 potentials, then the
> minimization occurs without error, but the structure has poor base
> stacking.  Any help would be greatly appreciated.
>
> Thanks,
>
> Gokul
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